As a method of detecting a small amount of gene in a sample, there is known a polymerase chain reaction method to amplify a gene using enzymes for nucleic acid synthesis, and a number of further improved methods for gene detection have been reported. Meanwhile, there have been reported some methods of detecting a gene by hybridizing oligonucleotides obtained by branching a single-stranded DNA, or the like (Non-Patent Documents 1 and 2).
On the other hand, Usui et al. have reported a novel isothermal nucleic acid amplification method using no enzyme (Patent Documents 1 to 4). This method is intended to form an assembly (polymer) of probes by a self-assembly reaction of plural kinds of oligonucleotides (referred to as probes) that have base sequence regions complementary to each other and is applied to detection of a test gene in a sample by quantification of the polymer. For example, if one of complementary base sequence regions of a probe to be used is designed so as to be a base sequence complementary to a test gene in a sample, this method can detect the test gene effectively by binding the probe to the test gene and then forming a polymer of probes, and it is referred to as PALSAR method.
The PALSAR methods are broadly classified into three groups depending on the kinds of probes to be used. The probes of the first group are two oligonucleotides (referred to as probe-1 and probe-2) which are represented by the following chemical formulas (1) and (2) and which include three complementary base sequence regions, and the regions X and X′, Y and Y′, and Z and Z′ independently have base sequences complementary to each other, so the oligonucleotides can complementarily bind to each other, to thereby form a polymer represented by the following chemical formula (9) (Patent Documents 1 and 2, hereinafter, referred to as PALSAR I).

The probes of the second group are two kinds of probes (referred to as dimer probe-1 and dimer probe-2) which are represented by the following chemical formulas (3) and (4) and have complementary base sequence regions, and if the regions A and A′, B and B′, C and C′, D and D′, E and E′, and F and F′ are designed so as to independently have complementary base sequence regions, the probes can complementarily bind to each other, to thereby form a polymer represented by the chemical formula (9) (Patent Document 3, hereinafter, referred to as PALSAR II).

The probes of the third group are one dimer probe (referred to as dimer probe-3) represented by the following chemical formula (6) and two oligonucleotides (referred to as crosslinking probes) represented by the following chemical formula (7), and if the regions A and A′, B and B′, C and C′, D and D′, and F and F′ are designed so as to independently have complementary base sequence regions, the dimer probe and the oligonucleotides can complementarily bind to each other, to thereby form a polymer represented by the chemical formula (10) (Patent Document 4, hereinafter, referred to as PALSAR III).

An example of methods of detecting a test gene in a sample using the PALSAR methods will be described below. For example, in the case of using two kinds of probes, a capture oligonucleotide immobilized to a support is allowed to react with a sample, to thereby capture the gene. In this case, the capture oligonucleotide has a base sequence region complementary to that of the test gene. Subsequently, one probe that has a base sequence region complementary to the base sequence of the gene (other than the part to bind to the capture oligonucleotide) is allowed to react to bind to the gene. Subsequently, both the probes having abilities to complementarily bind to each other are added to form a polymer, and the polymer is quantified to determine the gene.
However, in this unique PALSAR method, if a polymer formation reaction is performed using a reaction solution containing plural kinds of probes having abilities to complementarily bind to each other, the polymer may be formed at a site other than the captured test gene, i.e., in the state of unbound to the test gene, resulting in nonspecific signals that affect quantitative characteristics.
Patent Document 1: Japanese Patent No. 3,267,576
Patent Document 2: International Publication No. WO 01/75157
Patent Document 3: International Publication No. WO 02/31192
Patent Document 4: Published Japanese Application No. 2002-355081
Non-patent Document 1: Shchepinov et. al, Nuc. Acids Res. 1997, 25, 4447-4454
Non-patent Document 2: Stears et. al, Physiol. Genomics, 2000, 3:93-99